Package org.snpeff.geneOntology

Class GoTerm

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<GoTerm>, java.lang.Iterable<java.lang.String>
    public class GoTerm
extends java.lang.Object
implements java.lang.Comparable<GoTerm>, java.lang.Iterable<java.lang.String>, java.io.Serializable
    An instance of a GO term (a node in the DAG)
    Author:
    Pablo Cingolani
    See Also:
    Serialized Form

    • Field Detail

      • debug

        public static boolean debug

    • Constructor Detail

      • GoTerm

        public GoTerm​(java.util.List<GoTerm> goTermList,
              GoTerms goTerms)
        Create a new GOTerm by joining all GOTerms in the list
        Parameters:
        goTermList -

      • GoTerm

        public GoTerm​(java.lang.String acc,
              GoTerms goTerms,
              java.lang.String nameSpace,
              java.lang.String description)

    • Method Detail

      • addChild

        public void addChild​(GoTerm childGoTerm)
        Add a goTermId as a child of this GOTerm Also adds 'this' as parent of 'goTerm'
        Parameters:
        goTermAcc -

      • addInterestingSymbolId

        public void addInterestingSymbolId​(java.lang.String symbolId)
        Add one gene to interestingGenesSet
        Parameters:
        symbolId -

      • addSymbolId

        public void addSymbolId​(java.lang.String symbolId)
        Add one gene to genesSet
        Parameters:
        symbolId -

      • addSymbolsFromChilds

        public void addSymbolsFromChilds​(GoTerm goTerm)
        Add all symbols from childs to goTerm

      • compareTo

        public int compareTo​(GoTerm goTerm)
        Specified by:
        compareTo in interface java.lang.Comparable<GoTerm>

      • getAcc

        public java.lang.String getAcc()

      • getChilds

        public java.util.HashSet<GoTerm> getChilds()

      • getDescription

        public java.lang.String getDescription()

      • getFirstChild

        public GoTerm getFirstChild()
        Return first child in the list
        Returns:
        First child (or null if there are no children)

      • getFirstParent

        public GoTerm getFirstParent()
        Return first parent in the list
        Returns:
        First parent (or null if there are no parents)

      • getGoTerms

        public GoTerms getGoTerms()

      • getInterestingSymbolIdSet

        public java.util.HashSet<java.lang.String> getInterestingSymbolIdSet()

      • getInterestingSymbolIdsSize

        public int getInterestingSymbolIdsSize()
        Number of 'interesting' symbols
        Returns:

      • getLevel

        public int getLevel()
        Calculate node's level
        Returns:

      • getMaxRank

        public int getMaxRank()

      • getNameSpace

        public java.lang.String getNameSpace()

      • getParents

        public java.util.HashSet<GoTerm> getParents()

      • getRankedSymbols

        public int getRankedSymbols()

      • getSymbolIdSet

        public java.util.Set<java.lang.String> getSymbolIdSet()
        Number of symbols in this node (total = interesting + not-interesting)
        Returns:

      • getTotalCount

        public int getTotalCount()
        Number of symbols in this node (total = interesting + not-interesting)
        Returns:

      • intersection

        public void intersection​(GoTerm goTerm)
        Intersects this term with 'goTerm' (intersects 'symbolIdSet' and 'interestingSymbolIdSet').
        Parameters:
        goTerm - : GOTerm to intercept

      • isLeave

        public boolean isLeave()
        Is this GOTerm a leave?
        Returns:

      • iterator

        public java.util.Iterator<java.lang.String> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<java.lang.String>

      • rootNode

        public GoTerm rootNode()
        Get the root node
        Returns:

      • setAcc

        public void setAcc​(java.lang.String go)

      • setChilds

        public void setChilds​(java.util.HashSet<GoTerm> childs)

      • setGenesSet

        public void setGenesSet​(java.util.HashSet<java.lang.String> genesSet)

      • setGoTerms

        public void setGoTerms​(GoTerms goTerms)

      • setInterestingSymbolIdSet

        public void setInterestingSymbolIdSet​(java.util.HashSet<java.lang.String> interestingSymbolIdSet)

      • setLevel

        public void setLevel​(int level)

      • setMaxRank

        public void setMaxRank​(int maxRank)

      • setMinus

        public void setMinus​(GoTerm goTerm)
        Perform a 'set minus' between this term and 'goTerm' (set minus for 'symbolIdSet' and 'interestingSymbolIdSet').
        Parameters:
        goTerm - : GOTerm to use for 'set minus' operation

      • setNameSpace

        public void setNameSpace​(java.lang.String goTermType)

      • setParents

        public void setParents​(java.util.HashSet<GoTerm> parents)

      • setRankedSymbols

        public void setRankedSymbols​(int rankedSymbols)

      • setRankSum

        public void setRankSum​(int rankSum)

      • setSescription

        public void setSescription​(java.lang.String description)

      • setSymbolIdSet

        public void setSymbolIdSet​(java.util.HashSet<java.lang.String> symbolIdSet)

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toStringAll

        public java.lang.String toStringAll()

      • toStringAll

        public java.lang.String toStringAll​(boolean showSymbols)

      • union

        public void union​(GoTerm goTerm)
        Union this term with 'goTerm' (union for 'symbolIdSet' and 'interestingSymbolIdSet').
        Parameters:
        goTerm - : GOTerm to use for union